Hello
Sex was protected and it should be without any disease ( since you were taken every precaution).
In the beginning all the tests were NEGATIVE .
While window period for HIV is 90 days and this negative , so no chance of getting any HIV by you>
Now about syphilis , the 
incubation period is 10-90 days  .
As you mentioned that there is rash on the arm and a small lump on the vagina .
However, the incubation period for 
secondary syphilis is 2 to 18 weeks but in your case these symptoms are NOT an indication of syphilis ,so don't worry . 
For your surety I am writing symptoms of secondary syphilis , these are .
Fever, 
malaise, decreased appetite, GENERALIZED 
LYMPHADENOPATHY, rash ( maculopapular) may be pustular, .It starts in the trunk and then spreads to palm and soles .
I mentioned all these symptoms ,so that you get relief that you are not having such type of any disease .
So be confident .
Good luck.